AbsorberPlotter

class salsa.AbsorberPlotter(abs_ext, ion_name='H I', ftype='gas', absorber_fields=[], markers=True, mark_plot_args=None, figure=None)

Bases: object

Create’s plot to easily see where absorbers are found along the light ray both directly and through resulting spectra. Uses absorber extractor as base class.

Parameters:

  • abs_ext (AbsorberExtractor object) – Absorber extractor used to extract the data we want to plot. Can be any of the child classes; e.g. SPICEAbsorberExtractor

  • ion_name (string, optional) – Name of the ion to extract absorbers of and plot Default: “H I”

  • ftype (string, optional) – Field type for ion fields. Allows ion fields to be added if not already present. Default: “gas”

  • absorber_fields (list of strings, optional) – Additional ions to include in plots/Spectra, enter as list.

  • markers (bool, optional) – whether to include markers on light ray and number density plot

  • mark_plot_args (dict, optional) –

    set the property of markers if they are to be plotted. optional settings are:

    marker_spacing: determines how far apart markers are in kpc.

    marker_shape: shape of marker see matplotlib for notation

    marker_cmap: colormap used to differentiate markers any other property that can be passer to matplotlib scatter

  • figure (matplotlib figure, optional) – where the multi_plot will be plotted. creates one if none is specified.

Notes

ion names should be in following notaion: neutral Hydrogen–>”H I”, 5-times ionized Oxygen –> “O VI”

Methods Summary

close()

close all opened files

create_slice([center, slice_field, ...])

Create a slice in the Dataset along the path of the ray.

plot_lambda_space([wavelength_width, ...])

Use trident to plot the absorption spectrum of the ray.

plot_multiplot([outfname, center, ...])

Combines the slice plot, number density plot, and (optionally) spectrum plot into one image and saves it to disk.

plot_num_density(ax_num_dense[, ...])

Plots the number density at different lengths along the ray

plot_vel_space([velocity_width, ax_vel])

Use trident to plot the absorption spectrum of the ray in velocity space.

Methods Documentation

close()

close all opened files

create_slice(center=None, slice_field=None, north_vector=[0, 0, 1], plot_ray=True, cmap='magma', height=None, width=None)

Create a slice in the Dataset along the path of the ray. Choose to keep the Z direction maintained.

Parameters:

  • center (array type, optional) – Center of the slice in code_length. If None, then defaults to domain_center

  • slice_field (string, optional) – Field to plot. Defaults to the number density for the ion associated with the abs_ext attribute.

  • north_vector (array type, optional) – vector used to fix the orientation of the slice plot. Defaults to z-axis

  • plot_ray (bool) – Whether to annotate ray/markers to the slice plot or to just calculate the marker positions for placing on los_velocity plot

  • cmap (str) – the colormap to use for the slice. Default: ‘magma’

  • height (float, optional) – dimension for the figure

  • width (float, optional) – dimension for the figure

Returns:

slice – Slice with ray annotated. This SlicePlot is also saved to the .slice attribute.

Return type:

yt SlicePlot

plot_lambda_space(wavelength_width=30, wavelength_res=0.1, ax=None, **kwargs)

Use trident to plot the absorption spectrum of the ray. Plot in wavelegnth (lambda) space.

Parameters:

  • wavelength_width (float, optional) – sets the wavelength range of the spectrum plot. defaults to 300 Angstroms

  • wavelength_res (float, optional) – width of wavelength bins in spectrum plot. default 0.1 Angstrom

  • ax (matplotlib axis) – axis in which to draw the spectra plot

Returns:

  • wavelength (YT array) – Array of wavelength values of the generated spectra (in km/s)

  • flux (YT array) – Array of the normalized flux values of the generated spectra

plot_multiplot(outfname=None, center=None, slice_field=None, north_vector=[0, 0, 1], cmap='magma', make_spectra=True, plot_spice_intervals=True, annotate_column_density=True, velocity_width=3000, **kwargs)

Combines the slice plot, number density plot, and (optionally) spectrum plot into one image and saves it to disk.

Can supply any optional keyword arguments supported by plot_num_density and plot_vel_space.

Parameters:

  • outfname (str , optional) – the file name/path in which to save the file defaults to being unsaved. Default: None

  • gal_center (array type, optional) – Center of the slice in code_length. If None, then defaults to domain_center

  • slice_field (string, optional) – Field to plot. Defaults to the number density for the ion associated with the abs_ext attribute.

  • north_vector (array type, optional) – vector used to fix the orientation of the slice plot. Defaults to z-axis

  • cmap (Colormap, optional) – the color map to use for the slice plot. Default: magma

  • plot_spice_intervals (bool, optional) – whether or not to shade the absorber intervals found by SPICE in the number density plot

  • make_spectrum (bool, optional) – whether to include the spectrum plot or not. Given that the transition from yt 3 to yt 4 has affected Trident’s spectra generation (https://github.com/trident-project/trident/issues/217), you may wish to not include this plot. Default: True

  • annotate_column_density (bool, optional) – whether or not to annotate the column densities of absorbers in the spectrum plot

  • velocity_width (float, optional) – velocity range of the spectrum plot in km/s

Returns:

  • fig (matplotlib figure:) – figure multi_plot is drawn on

  • axes (matplotlib axes) – axes the three lower plots are drawn on

plot_num_density(ax_num_dense, num_dense_min=None, num_dense_max=None, ax_prop2=None, prop2_name='velocity_los', prop2_units=None, plot_spice_intervals=False, plot_kwargs={}, **kwargs)

Plots the number density at different lengths along the ray

Parameters:

  • ax_num_dense (matplotlib axis) – axis in which to draw the number density plot

  • num_dense_min (float, optional) – Sets the lower limit for the number density plot. If None, defaults to 0.01 times the median number density

  • num_dense_max (float, optional) – Sets the upper limit for the number density plot. If None, defaults to 100 times the median number density

  • ax_prop2 (matplotlib axis, optional) – axis in which to draw the second field. if None, no plot is made Default: None

  • prop2_name (str, optional) – Field to plot in second plot. Default:’velocity_los’

  • prop2_units (str, optional) – The units to use in the second field. Defaults: None

  • plot_spice_intervals (bool, optional) – If using a SPICEAbsorberExtractor, plot the SPICE intervals. Has no effect for any other AbsorberExtractor class.

  • plot_kwargs (dict, optional) – A Dictionary of plot kwargs to be passed to the pyplot.plot function. Default: {}

plot_vel_space(velocity_width=3000, ax_vel=None, **kwargs)

Use trident to plot the absorption spectrum of the ray in velocity space. Uses the wavelength centers and velocity resolution of the AbsorberExtractor to generate the spectrum.

Parameters:

  • velocity_width (float, optional) – sets the velocity range of spectrum plot in units of km/s

  • ax_vel (matplotlib axis object, optional) – an axis in which to draw the velocity plot. If None, no plot is not drawn. Default: None

Returns:

  • velocity (YT array) – Array of velocity values of the generated spectra (in km/s)

  • flux (YT array) – Array of the normalized flux values of the generated spectra